Flatpak can do CLI apps it's just mildly unwieldy because of the whole flatpak run ....
If you want reproducible dev environments, yeah you're pushed to container solutions be it distrobox, Podman or Docker. Or something like nix as a user.
If you install a Debian distrobox it'll be as reliable as Debian itself is. It's only an issue when you're after 100% reproducible systems, which Docker can help somewhat with, or again, nix. Or NixOS if you really want it all system-wide.